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相关概念视频

Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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Immunoprecipitation01:20

Immunoprecipitation

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Immunoprecipitation, or IP, is a widely used technique that employs protein-antibody interactions to isolate proteins or protein complexes in their native state for studying protein-protein interactions, quaternary structures, or supramolecular complexes. Various modifications of the technique, including chromatin IP, cross-linking IP, and fluorescence IP, are commonly used.
Chromatin Immunoprecipitation
Chromatin immunoprecipitation, also known as ChIP, is used to study protein-DNA or...
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相关实验视频

Updated: Jul 10, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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ProtWave-VAE:集成自回归采样与基于潜伏的推理,用于数据驱动的蛋白质设计.

Nikša Praljak1, Xinran Lian2, Rama Ranganathan3,4

  • 1Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois 60637, United States.

ACS synthetic biology
|November 21, 2023
PubMed
概括

ProtWave-VAE是一种新的深度生成模型,通过结合变异自编码器和自回归模型,有效地设计蛋白质. 这种方法可以从未对齐的序列数据中创建功能合成蛋白质.

关键词:
深度生成建模 深度生成建模蛋白质设计 蛋白质设计合成生物学 合成生物学

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科学领域:

  • 计算生物学是一种计算生物学.
  • 蛋白质工程是一种蛋白质工程.
  • 机器学习是机器学习.

背景情况:

  • 像VAE和AR模型这样的深度生成模型 (DGM) 用于蛋白质设计.
  • VAE从对齐序列 (MSA) 中学习,并创建潜在空间.
  • 增强现实模型处理不对齐的序列和可变长度,但缺乏隐藏空间.

研究的目的:

  • 介绍ProtWave-VAE,这是一个结合VAE和AR优势的新型DGM.
  • 能够在未对齐的序列上进行训练,并设计可变长度的蛋白质.
  • 为蛋白质设计生成可解释的潜伏空间.

主要方法:

  • 开发了ProtWave-VAE,使用信息最大化的VAE与扩展卷积编码器和WaveNet解码器.
  • 训练并评估了对无对齐的同类蛋白质家族的模型.
  • 应用该模型来设计合成蛋白质和工程功能.

主要成果:

  • ProtWave-VAE成功地推断了潜伏空间中的功能和遗传学模式.
  • 该模型在半监督的健身预测任务中实现了高精度.
  • 实验验证证了功能合成蛋白质的设计,包括在SH3领域的工程化透传感.

结论:

  • 在蛋白质设计中,ProtWave-VAE有效地结合了VAE和AR模型的优势.
  • 该模型可以从未对齐的序列数据中设计出新型的功能性蛋白质.
  • ProtWave-VAE使蛋白质的条件设计和功能工程成为可能.